Networks

StringDB Network

StringDB Network

GENEMania Network

GENEMania Network

List of genes from two network sources

## Cache found

PheWAS of genes

AAMP

## [1] "Number of data points: 245"
## 
## Not.Signi     Signi 
##       203        42

ACE

## [1] "Number of data points: 323"
## 
## Not.Signi     Signi 
##       300        23

ACE2

## [1] "Number of data points: 64"
## 
## Not.Signi 
##        64

AGT

## [1] "Number of data points: 393"
## 
## Not.Signi     Signi 
##       380        13

CAT

## [1] "Number of data points: 228"
## 
## Not.Signi     Signi 
##       226         2

DPEP1

## [1] "Number of data points: 466"
## 
## Not.Signi     Signi 
##       400        66

DPP4

## [1] "Number of data points: 477"
## 
## Not.Signi     Signi 
##       431        46

GHRL

## [1] "Number of data points: 314"
## 
## Not.Signi     Signi 
##       311         3

ISYNA1

## [1] "Number of data points: 425"
## 
## Not.Signi     Signi 
##       393        32

KDM3A

## [1] "Number of data points: 342"
## 
## Not.Signi     Signi 
##       292        50

LACTB2

## [1] "Number of data points: 376"
## 
## Not.Signi     Signi 
##       357        19

MEP1A

## [1] "Number of data points: 243"
## 
## Not.Signi 
##       243

MEP1B

## [1] "Number of data points: 237"
## 
## Not.Signi     Signi 
##       236         1

MME

## [1] "Number of data points: 296"
## 
## Not.Signi     Signi 
##       294         2

PDE9A

## [1] "Number of data points: 366"
## 
## Not.Signi     Signi 
##       360         6

POU2F1

## [1] "Number of data points: 314"
## 
## Not.Signi     Signi 
##       307         7

PRCP

## [1] "Number of data points: 313"
## 
## Not.Signi     Signi 
##       308         5

RASEF

## [1] "Number of data points: 257"
## 
## Not.Signi     Signi 
##       254         3

SLC10A2

## [1] "Number of data points: 275"
## 
## Not.Signi     Signi 
##       273         2

SLC12A6

## [1] "Number of data points: 309"
## 
## Not.Signi     Signi 
##       308         1

SLC37A1

## [1] "Number of data points: 347"
## 
## Not.Signi     Signi 
##       346         1

SLC44A4

## [1] "Number of data points: 957"
## 
## Not.Signi     Signi 
##       682       275

TMEM27

## [1] "Number of data points: 80"
## 
## Not.Signi     Signi 
##        79         1

TMPRSS2

## [1] "Number of data points: 227"
## 
## Not.Signi 
##       227

TRPM4

## [1] "Number of data points: 252"
## 
## Not.Signi     Signi 
##       249         3

XPNPEP2

## [1] "Number of data points: 83"
## 
## Not.Signi 
##        83

Gene Prioritization

Look at distribution of genes for significant traits grouped by domains

Enrichment test for domains

## Warning: Factor `Domain` contains implicit NA, consider using
## `forcats::fct_explicit_na`
##      [,1] [,2]
## [1,]   23  580
## [2,]   65 7541
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 5.056e-08
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  2.943958      Inf
## sample estimates:
## odds ratio 
##   4.599068 
## 
##      [,1] [,2]
## [1,]   23  580
## [2,]   89 7517
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 5.004e-06
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  2.175402      Inf
## sample estimates:
## odds ratio 
##   3.348489 
## 
##      [,1] [,2]
## [1,]    4  599
## [2,]   18 7588
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.07326
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.8720545       Inf
## sample estimates:
## odds ratio 
##   2.814315 
## 
##      [,1] [,2]
## [1,]  131  472
## [2,]  618 6988
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  2.611158      Inf
## sample estimates:
## odds ratio 
##   3.137656 
## 
##      [,1] [,2]
## [1,]    1  602
## [2,]    5 7601
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.3674
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.1082271       Inf
## sample estimates:
## odds ratio 
##   2.524819 
## 
##      [,1] [,2]
## [1,]   22  581
## [2,]  136 7470
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.002626
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  1.358581      Inf
## sample estimates:
## odds ratio 
##   2.079583 
## 
##      [,1] [,2]
## [1,]   38  565
## [2,]  267 7339
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.0008479
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  1.345597      Inf
## sample estimates:
## odds ratio 
##   1.848604 
## 
##      [,1] [,2]
## [1,]   29  574
## [2,]  250 7356
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.03554
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  1.035915      Inf
## sample estimates:
## odds ratio 
##   1.486484 
## 
##      [,1] [,2]
## [1,]    9  594
## [2,]   79 7527
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.1961
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.7256136       Inf
## sample estimates:
## odds ratio 
##   1.443526 
## 
##      [,1] [,2]
## [1,]   13  590
## [2,]  126 7480
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.2203
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.7508961       Inf
## sample estimates:
## odds ratio 
##   1.307995 
## 
##      [,1] [,2]
## [1,]   71  532
## [2,]  764 6842
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.1014
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.9500717       Inf
## sample estimates:
## odds ratio 
##   1.195145 
## 
##      [,1] [,2]
## [1,]    8  595
## [2,]   89 7517
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.4206
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.5473077       Inf
## sample estimates:
## odds ratio 
##   1.135586 
## 
##      [,1] [,2]
## [1,]    3  600
## [2,]   35 7571
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.5361
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.2813018       Inf
## sample estimates:
## odds ratio 
##   1.081529 
## 
##      [,1] [,2]
## [1,]   11  592
## [2,]  139 7467
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.548
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.545617      Inf
## sample estimates:
## odds ratio 
##  0.9981652 
## 
##      [,1] [,2]
## [1,]  143  460
## [2,] 2008 5598
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.9332
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.7315175       Inf
## sample estimates:
## odds ratio 
##  0.8666767 
## 
##      [,1] [,2]
## [1,]   24  579
## [2,]  357 7249
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.8154
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.5693457       Inf
## sample estimates:
## odds ratio 
##  0.8416654 
## 
##      [,1] [,2]
## [1,]    1  602
## [2,]   15 7591
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.7053
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.04042322        Inf
## sample estimates:
## odds ratio 
##  0.8406511 
## 
##      [,1] [,2]
## [1,]    9  594
## [2,]  136 7470
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.7477
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.4239442       Inf
## sample estimates:
## odds ratio 
##  0.8322241 
## 
##      [,1] [,2]
## [1,]    9  594
## [2,]  138 7468
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.7619
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.4178009       Inf
## sample estimates:
## odds ratio 
##  0.8199427 
## 
##      [,1] [,2]
## [1,]    4  599
## [2,]   62 7544
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.7246
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.2688284       Inf
## sample estimates:
## odds ratio 
##  0.8125442 
## 
##      [,1] [,2]
## [1,]    9  594
## [2,]  169 7437
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.9144
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.3409173       Inf
## sample estimates:
## odds ratio 
##  0.6668084 
## 
##      [,1] [,2]
## [1,]    2  601
## [2,]   49 7557
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.8977
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.08859874        Inf
## sample estimates:
## odds ratio 
##  0.5132864 
## 
##      [,1] [,2]
## [1,]    3  600
## [2,]   84 7522
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 0.9596
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.1194428       Inf
## sample estimates:
## odds ratio 
##  0.4477696 
## 
##      [,1] [,2]
## [1,]   10  593
## [2,]  767 6839
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 1
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.08088351        Inf
## sample estimates:
## odds ratio 
##  0.1503816 
## 
##      [,1] [,2]
## [1,]    3  600
## [2,] 1094 6512
## 
##  Fisher's Exact Test for Count Data
## 
## data:  datad
## p-value = 1
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
##  0.008086811         Inf
## sample estimates:
## odds ratio 
## 0.02976635

The distribution of genes in immunological domain

The distribution of genes in metabolic domain

Variant prioritization of priortized genes

Finding SNPs that are within +/- 10kb of the gene positions

Functional annotation of SNPs

CADD Scores

eQTLs

Tissue based distribution

RegulomeDB

Venn Diagram of all SNPs that were priortized using each of the annotations

Tabular distribution